Function of chloroplast RNA-binding proteins

Jacobs, Jessica; Kück, Ulrich

doi:10.1007/s00018-010-0523-3

Cited by 35 publications

(31 citation statements)

References 141 publications

(177 reference statements)

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“…The other GUN protein, GUN1, is a plastid-localized PPR protein (60). PPR proteins belong to a large family (>450 members) of RNA-binding proteins that typically function in RNA processing in plastids and mitochondria (24,44). In one model, GUN1 promotes the activity of the transcriptional regulator ABSCISIC ACID INSENSITIVE 4 (ABI4) to inhibit the nuclear transcription of LIGHT HARVESTING COMPLEX B (LHCB) genes (62).…”

Section: Discussionmentioning

confidence: 99%

“…The RNA levels reflect transcription as well as RNA processing and stability. For example, there is limited transcriptional regulation of gene expression in mitochondrial and plastid genomes (24). It is also well known that differences in RNA levels do not necessarily reflect changes in protein content.…”

Section: Ise2 Is Found In Chloroplastsmentioning

confidence: 99%

“…The ISE1 and ISE2 RNA helicases likely are involved in processing transcripts of mitochondrial and plastid-encoded genes, respectively. Posttranscriptional modification and modulation of transcripts are major strategies for controlling expression of mitochondrial and plastid genes (24,40). We therefore anticipated modest changes in the levels of organelle-encoded transcripts.…”

Section: Ise2 Is Found In Chloroplastsmentioning

confidence: 99%

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Organelle–nucleus cross-talk regulates plant intercellular communication via plasmodesmata

Burch‐Smith¹,

Brunkard²,

Choi

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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We use Arabidopsis thaliana embryogenesis as a model system for studying intercellular transport via plasmodesmata (PD). A forward genetic screen for altered PD transport identified increased size exclusion limit (ise) 1 and ise2 mutants with increased intercellular transport of fluorescent 10-kDa tracers. Both ise1 and ise2 exhibit increased formation of twinned and branched PD. ISE1 encodes a mitochondrial DEAD-box RNA helicase, whereas ISE2 encodes a DEVH-type RNA helicase. Here, we show that ISE2 foci are localized to the chloroplast stroma. Surprisingly, plastid development is defective in both ise1 and ise2 mutant embryos. In an effort to understand how RNA helicases that localize to different organelles have similar impacts on plastid and PD development/function, we performed whole-genome expression analyses. The most significantly affected class of transcripts in both mutants encode products that target to and enable plastid function. These results reinforce the importance of plastid-mitochondria-nucleus cross-talk, add PD as a critical player in the plant cell communication network, and thereby illuminate a previously undescribed signaling pathway dubbed organelle-nucleus-plasmodesmata signaling. Several genes with roles in cell wall synthesis and modification are also differentially expressed in both mutants, providing new targets for investigating PD development and function.

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Section: Discussionmentioning

confidence: 99%

Section: Ise2 Is Found In Chloroplastsmentioning

confidence: 99%

Section: Ise2 Is Found In Chloroplastsmentioning

confidence: 99%

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Organelle–nucleus cross-talk regulates plant intercellular communication via plasmodesmata

Burch‐Smith¹,

Brunkard²,

Choi

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

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“…With respect to the decreased levels of plastid mRNAs seen in L. polyedrum cysts, the decrease in mRNAs encoding pentatricopeptide repeat (PPR) family proteins mRNAs in Arabidopsis (Chiba et al, 2013) may be a useful model. PPR proteins are nuclear-encoded proteins that are directed to organelles, where they are responsible for stabilizing organelle-encoded transcripts (Jacobs and Kück, 2011). However, in L. polyedrum, no nuclearencoded mRNAs for plastid-directed proteins were specifically degraded under cold stress.…”

Section: Discussionmentioning

confidence: 99%

Cold-Induced Cysts of the Photosynthetic DinoflagellateLingulodinium polyedrumHave an Arrested Circadian Bioluminescence Rhythm and Lower Levels of Protein Phosphorylation

2013

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Dinoflagellates are microscopic, eukaryotic, and primarily marine plankton. Temporary cyst formation is a well-known physiological response of dinoflagellate cells to environmental stresses. However, the molecular underpinnings of cold-induced cyst physiology have never been described. Cultures of the photosynthetic dinoflagellate Lingulodinium polyedrum readily form temporary cysts when placed at low (8°C 6 1°C) temperature and excyst to form normal motile cells following a return to normal temperature (18°C 6 1°C). The normal circadian bioluminescence rhythm and the expected changes in Luciferin Binding Protein abundance were arrested in L. polyedrum cysts. Furthermore, after excystment, the bioluminescence rhythm initiates at a time corresponding to zeitgeber 12, independent of the time when the cells encysted. Phosphoprotein staining after two-dimensional polyacrylamide gel electrophoresis, as well as column-based phosphoprotein enrichment followed by liquid chromatography tandem mass spectrometry, showed cyst proteins are hypophosphorylated when compared with those from motile cells, with the most marked decreases found for predicted Casein Kinase2 target sites. In contrast to the phosphoproteome, the cyst proteome is not markedly different from motile cells, as assessed by two-dimensional polyacrylamide gel electrophoresis. In addition to changes in the phosphoproteome, RNA sequencing revealed that cysts show a significant decrease in the levels of 132 RNAs. Of the 42 RNAs that were identified by sequence analysis, 21 correspond to plastid-encoded gene products and 11 to nuclear-encoded cell wall/plasma membrane components. Our data are consistent with a model in which the highly reduced metabolism in cysts is achieved primarily by alterations in the phosphoproteome. The stalling of the circadian rhythm suggests temporary cysts may provide an interesting model to address the circadian system of dinoflagellates.

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“…Interestingly, low-complexity regions also occur in other psaA-splicing factors such as Raa4, which harbors alanine-and glutamine-rich regions (14). Another similarity to Raa4 is the absence of typical RNAbinding domains such as the K homology domain, the RNA recognition motif, the CRM domain, and pentatricopeptide repeats (57,58). Nevertheless, we demonstrated the direct binding of Rab1 to psaA intron RNA via electromobility shift assays.…”

Section: Discussionmentioning

confidence: 99%

Identification of a Chloroplast Ribonucleoprotein Complex Containing Trans-splicing Factors, Intron RNA, and Novel Components

Jacobs

Marx

Kock

et al. 2013

Molecular & Cellular Proteomics

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Maturation of chloroplast psaA pre-mRNA from the green alga Chlamydomonas reinhardtii requires the trans-splicing of two split group II introns. Several nuclear-encoded trans-splicing factors are required for the correct processing of psaA mRNA. Among these is the recently identified Raa4 protein, which is involved in splicing of the tripartite intron 1 of the psaA precursor mRNA. Part of this tripartite group II intron is the chloroplast encoded tscA RNA, which is specifically bound by Raa4. Using Raa4 as bait in a combined tandem affinity purification and mass spectrometry approach, we identified core components of a multisubunit ribonucleoprotein complex, including three previously identified trans-splicing factors (Raa1, Raa3, and Rat2). We further detected tscA RNA in the purified protein complex, which seems to be specific for splicing of the tripartite group II intron. Intron-containing genes from prokaryotic or organellar genomes carry either group I or group II introns, each of which has distinct features. The splicing mechanism of group II introns and the secondary structures of their presumed active sites were used as early arguments for the hypothesis that this class of introns represents the ancestors of eukaryotic spliceosomal introns (1, 2). It was further assumed that group II introns invaded the eukaryotic nucleus and subsequently proliferated at various genomic sites, leading to the degeneration of the catalytic intron structure into small nuclear RNAs (snRNAs).1 This assumption was supported by the observation of naturally occurring variants of group II introns that are split into two or more pieces (3), reminiscent of eukaryotic spliceosomal RNA (1). Group II intron RNAs are characterized by six conserved domains, and tertiary interactions among these domains generate the compact native and catalytic complex. Some of these group II intron domains have been shown to act in trans on the splicing of other introns that lack the corresponding domain (4). In vivo, various RNA-binding proteins promote the formation of catalytically active intron RNA. In contrast to the nuclear spliceosome, which acts generally on a broad range of nuclear-encoded pre-mRNAs, proteins involved in organellar intron splicing seem to more efficiently stabilize the active three-dimensional RNA structure in vivo. Several splicing factors in higher plants, such as the chloroplast RNA-splicing and ribosome maturation (CRM) domain protein CRS1, as well as the pentatricopeptide repeat proteins OTP51 and PPR4, have been reported to be involved in the splicing of single transcripts (5, 6). Nonetheless, there are splicing factors that carry out functions on a broad range of transcripts, including CRS2 and its associated proteins CAF1 and CAF2, and WTF1, a splicing factor containing a plant organelle RNA-recognition domain (5, 6). Sedimentation and co-fractionation experiments in, for example, maize have demonstrated that these proteins are part of large multiprotein and ribonucleoprotein complexes with their cognate RNAs (5, 7). I...

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Function of chloroplast RNA-binding proteins

Cited by 35 publications

References 141 publications

Organelle–nucleus cross-talk regulates plant intercellular communication via plasmodesmata

Organelle–nucleus cross-talk regulates plant intercellular communication via plasmodesmata

Cold-Induced Cysts of the Photosynthetic DinoflagellateLingulodinium polyedrumHave an Arrested Circadian Bioluminescence Rhythm and Lower Levels of Protein Phosphorylation

Identification of a Chloroplast Ribonucleoprotein Complex Containing Trans-splicing Factors, Intron RNA, and Novel Components

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